Reciprocal Pairs

Analysis of pairs of neurons (or partial neurons) that synapse onto one another

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a reciprocal pair of neurons that synapse onto one another

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Summary Presentation

View the Reciprocal Pairs summary presentation.

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Contents

Notebooks and datatables

Use the list_of_all_reciprocal_pairs.ipynb notebook to list and analyze all the reciprocal synapses in the volume. A special thank you to Wanwen Zeng at Stanford for generating the dictionary code to generate the reciprocal synapse list.

Use the reciprocal_pairs_neurons_with_soma_in_volume.ipynb notebook to list and analyze all the reciprocal pairs of neurons that have an identified soma within the Layer 2/3 volume.

Use the reciprocal_pairs_synapse_visualizer.ipynb notebook to generate 2D and 3D visualizations (using matplotlib, meshparty and vtk) of synapses for a desired set of reciprocal pairs. Includes over a dozen example pairs.

The paired.csv datatable contains all the reciprocal pairs (n = 1998/2 = 999) in the entire volume, including all the partial processes as well.

The pairs_rm_v_g_na.csv datatable contains the reciprocal pairs where both pairs have an identified soma in the volume, filtering out vascular and glial cells (because these are mis-segmented synapses anyway!), as well as filtering out the partial proceses. This was generated using the 220309_cell_type_classification.csv datatable. Confession: due to my novice pandas skills, I found it more expedient to create the datatable in Excel using a simple vlookup function.

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Visualization examples

Martinotti-bipolar reciprocal pair

Martinotti-bipolar reciprocal pair

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View the pair in neuroglancer.

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The inhibitory Martinotti neuron makes two synapses onto another inhibitory bipolar neuron. In turn, the bipolar neuron makes eight synapses onto the Martinotti neuron. Closeup 3D views (using meshparty and vtk) and the original electron micrograph views (in Neuroglancer) of select synapses are shown as well.

3D view of Martinotti neuron synapses on a bipolar neuron

3D rendering of Martinotti synapses onto a bipolar neuron using vtk visualizer

Neuroglancer EM view of these two synapses

electron micrographs of Martinotti synapses onto the bipolar neuron

3D view of one of the bipolar neuron’s synapse onto a Martinotti neuron

3D rendering of bipolar synapse onto a Martinotti neuron using vtk visualizer

Neuroglancer EM view of this synapse

electron micrographs of a bipolar neuron synapse onto the Martinotti neuron